Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Prolactin regulatory element-binding protein.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g9619 g9619.t5 TTS g9619.t5 4305152 4305152
chr_1 g9619 g9619.t5 isoform g9619.t5 4305218 4306654
chr_1 g9619 g9619.t5 exon g9619.t5.exon1 4305218 4306502
chr_1 g9619 g9619.t5 cds g9619.t5.CDS1 4305218 4306502
chr_1 g9619 g9619.t5 exon g9619.t5.exon2 4306569 4306654
chr_1 g9619 g9619.t5 cds g9619.t5.CDS2 4306569 4306654
chr_1 g9619 g9619.t5 TSS g9619.t5 4306739 4306739

Sequences

>g9619.t5 Gene=g9619 Length=1371
ATGGGGTCGAAAAAGAACATGATAACCGATTGCCTTTTAGCCAAAGTAAATTTTCCACTT
TATGCTGCTGAAATGCTAACAAGCAGACATTTGCTTGTCGCTGGTGGCGGTGGCTCAGCG
AAAACTGGAGTAGCAAATGGTTTTGAAATATATGAATTGTATCACAATGGAAAGTATTTT
GTGGCAGAAGAAATACAAAGACACGAAACAGGGTCAAGAGCCGTAATGAATATGTCATTA
AAACACATCGATCGAAGAGCACTGCTCGTTGCTGGTCAAGAAGGCCATAGTCAAATGTTT
GTTATCAGTTCAAAAGTAGGTCAATTGCCTACAAAAGAAACTCAAATTTCGAGTCGAAGG
GAATCATCATCAACGGAAGTTAGACAAAGAAGAAGAACAGAATCTACGAGTCAAGATACT
CCTAAATCTCAAATATCGACAACAACTGACTCCTCAGGAAATCAAATGAAACGAATTTAC
TTCGATATTAAAGCTGCCGATTCAGTACAAACAGATTTTTCTACTGAACCTTATCAAAGA
GTCGTGAGAATTTGTTTAAATGGAAAATTCATGGCAACAGCAGGAATTGATGGCCACGTT
CGTATATGGCATTTTCCACGAATGACACCATTTCATGATATAAAAGCTCATGAGAAAGAG
TTGGATGACTTGGATTTTAGTCCAGATGGCAAATACTTAATATCAATTGCAAAAGATGGT
ATTGCATCAGTTTGGTCAGTGAACAATGGAAAAGAGGCTTTGAAATTGAAATGGACACCA
CCAGAGAATGTTAAATATTTATATAAAAGATGTCGATATTCAACAATTGAAGGAGAAACA
GACAAATATAGACTCTTTACAATATCAAATCCACTACATAAAGCTGGAAAACAAAGAGGA
TTTTTGCAACAATGGAATATTGAGACTGGTCGACTCAATAATATAGTTAGCATAGATGAA
AGCCTTTCAGCATTAGCCGTTCGTGATGATGGTCGTTTTGTATCAATTGGAACAATGTTT
ACTGGTTCAGTTATGATTTATATTGCATTTAGTTTACAACAAGTGCTTTATGTGCCGAAT
GCTCATTCAATGTTTGTCACTGGTCTTGAATTTATTCCAGTTCTAAATAAAGATGCACCG
CCAATTTCAAGTGACGCTGAAGCTTCTGTTATATCATACTCTGTTGACAATCGTATCTGC
ATTCATAGTTTGCAATATAGACGTGAGTATATTTTATACAATATTTTATTTATATATTTA
TGCACAAACGTTTCTTTTTTTTCAGATACGTTGCCAGCATGGGCTGCAATATTTTTAATA
ATTGTTATTCTTTTCCTCACATTTTTAATGTGTTCTTACTTTGGTATATAA

>g9619.t5 Gene=g9619 Length=456
MGSKKNMITDCLLAKVNFPLYAAEMLTSRHLLVAGGGGSAKTGVANGFEIYELYHNGKYF
VAEEIQRHETGSRAVMNMSLKHIDRRALLVAGQEGHSQMFVISSKVGQLPTKETQISSRR
ESSSTEVRQRRRTESTSQDTPKSQISTTTDSSGNQMKRIYFDIKAADSVQTDFSTEPYQR
VVRICLNGKFMATAGIDGHVRIWHFPRMTPFHDIKAHEKELDDLDFSPDGKYLISIAKDG
IASVWSVNNGKEALKLKWTPPENVKYLYKRCRYSTIEGETDKYRLFTISNPLHKAGKQRG
FLQQWNIETGRLNNIVSIDESLSALAVRDDGRFVSIGTMFTGSVMIYIAFSLQQVLYVPN
AHSMFVTGLEFIPVLNKDAPPISSDAEASVISYSVDNRICIHSLQYRREYILYNILFIYL
CTNVSFFSDTLPAWAAIFLIIVILFLTFLMCSYFGI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g9619.t5 MobiDBLite mobidb-lite consensus disorder prediction 111 152 -
18 g9619.t5 MobiDBLite mobidb-lite consensus disorder prediction 123 137 -
19 g9619.t5 MobiDBLite mobidb-lite consensus disorder prediction 138 152 -
3 g9619.t5 PANTHER PTHR23284 PROLACTIN REGULATORY ELEMENT BINDING PROTEIN 13 453 6.3E-88
4 g9619.t5 PANTHER PTHR23284:SF0 PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN 13 453 6.3E-88
2 g9619.t5 Pfam PF00400 WD domain, G-beta repeat 185 203 0.083
1 g9619.t5 Pfam PF00400 WD domain, G-beta repeat 210 246 0.026
7 g9619.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 409 -
10 g9619.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 410 427 -
8 g9619.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 428 432 -
9 g9619.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 433 455 -
6 g9619.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 456 456 -
20 g9619.t5 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 187 255 16.296
21 g9619.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 214 255 13.449
15 g9619.t5 SMART SM00320 WD40_4 166 204 2.5
16 g9619.t5 SMART SM00320 WD40_4 207 246 8.3E-5
14 g9619.t5 SMART SM00320 WD40_4 352 403 78.0
5 g9619.t5 SUPERFAMILY SSF50978 WD40 repeat-like 180 407 4.07E-23
11 g9619.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 336 358 -
13 g9619.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 410 428 -
12 g9619.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 433 455 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values